Multiple sequence alignment - TraesCS2A01G432600

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G432600 chr2A 100.000 3890 0 0 1 3890 685753847 685749958 0.000000e+00 7184.0
1 TraesCS2A01G432600 chr2A 87.623 711 70 6 824 1533 137271680 137270987 0.000000e+00 809.0
2 TraesCS2A01G432600 chr2A 87.219 712 70 9 824 1533 660107864 660108556 0.000000e+00 791.0
3 TraesCS2A01G432600 chr2A 88.073 436 47 4 2672 3105 685741400 685740968 2.680000e-141 512.0
4 TraesCS2A01G432600 chr2A 95.820 311 12 1 1637 1947 660108628 660108937 5.800000e-138 501.0
5 TraesCS2A01G432600 chr2A 94.904 314 14 2 1637 1950 137270915 137270604 1.260000e-134 490.0
6 TraesCS2A01G432600 chr2A 86.105 439 50 7 2673 3111 685696602 685696175 2.740000e-126 462.0
7 TraesCS2A01G432600 chr2A 87.097 93 11 1 3435 3526 718386771 718386863 1.910000e-18 104.0
8 TraesCS2A01G432600 chr2A 98.113 53 1 0 1533 1585 137270966 137270914 4.140000e-15 93.5
9 TraesCS2A01G432600 chr2D 92.323 2475 145 23 652 3087 543048184 543045716 0.000000e+00 3476.0
10 TraesCS2A01G432600 chr2D 84.060 803 98 18 2332 3117 542946385 542945596 0.000000e+00 747.0
11 TraesCS2A01G432600 chr2D 88.618 369 32 8 2756 3117 543043600 543043235 1.280000e-119 440.0
12 TraesCS2A01G432600 chr2D 82.697 445 54 17 74 499 543055059 543054619 1.320000e-99 374.0
13 TraesCS2A01G432600 chr2D 77.512 209 24 5 3339 3525 56650920 56651127 1.910000e-18 104.0
14 TraesCS2A01G432600 chr2D 84.946 93 13 1 3434 3525 296906545 296906637 4.140000e-15 93.5
15 TraesCS2A01G432600 chr2B 89.963 2162 123 45 1655 3742 647742909 647740768 0.000000e+00 2704.0
16 TraesCS2A01G432600 chr2B 90.168 895 65 15 2307 3181 647707145 647706254 0.000000e+00 1144.0
17 TraesCS2A01G432600 chr2B 85.304 939 77 23 359 1296 647744100 647743222 0.000000e+00 913.0
18 TraesCS2A01G432600 chr2B 88.591 447 41 6 2672 3113 647735235 647734794 5.720000e-148 534.0
19 TraesCS2A01G432600 chr2B 88.263 426 43 5 2672 3097 647703964 647703546 1.610000e-138 503.0
20 TraesCS2A01G432600 chr2B 90.071 282 25 3 74 354 647744419 647744140 2.860000e-96 363.0
21 TraesCS2A01G432600 chr2B 86.391 169 18 2 3684 3847 647705948 647705780 3.090000e-41 180.0
22 TraesCS2A01G432600 chr2B 84.524 168 13 8 3174 3340 647706224 647706069 1.870000e-33 154.0
23 TraesCS2A01G432600 chr2B 78.571 210 21 11 3339 3526 265564063 265564270 2.460000e-22 117.0
24 TraesCS2A01G432600 chr2B 78.199 211 20 12 3339 3526 520209165 520209372 1.140000e-20 111.0
25 TraesCS2A01G432600 chr6D 88.592 710 63 6 824 1533 4873569 4872878 0.000000e+00 846.0
26 TraesCS2A01G432600 chr6D 94.921 315 13 3 1637 1950 4872806 4872494 1.260000e-134 490.0
27 TraesCS2A01G432600 chr6D 98.113 53 1 0 1533 1585 4872857 4872805 4.140000e-15 93.5
28 TraesCS2A01G432600 chr6D 88.000 50 6 0 74 123 80713752 80713703 4.200000e-05 60.2
29 TraesCS2A01G432600 chr5A 85.478 785 72 17 824 1585 12620334 12621099 0.000000e+00 780.0
30 TraesCS2A01G432600 chr5A 86.217 711 77 9 824 1533 69012724 69012034 0.000000e+00 750.0
31 TraesCS2A01G432600 chr5A 95.860 314 12 1 1637 1950 69011962 69011650 1.250000e-139 507.0
32 TraesCS2A01G432600 chr5A 95.820 311 12 1 1637 1947 12621098 12621407 5.800000e-138 501.0
33 TraesCS2A01G432600 chr5A 96.226 53 2 0 1533 1585 69012013 69011961 1.930000e-13 87.9
34 TraesCS2A01G432600 chr1A 86.639 711 76 5 824 1533 310699970 310700662 0.000000e+00 769.0
35 TraesCS2A01G432600 chr1A 94.855 311 15 1 1637 1947 310700734 310701043 5.840000e-133 484.0
36 TraesCS2A01G432600 chr1A 98.113 53 1 0 1533 1585 310700683 310700735 4.140000e-15 93.5
37 TraesCS2A01G432600 chr1A 92.000 50 4 0 74 123 301900475 301900524 1.940000e-08 71.3
38 TraesCS2A01G432600 chr4B 95.385 390 17 1 1637 2026 662856765 662857153 1.540000e-173 619.0
39 TraesCS2A01G432600 chr4B 82.885 520 68 7 1015 1533 662856194 662856693 7.670000e-122 448.0
40 TraesCS2A01G432600 chr4B 87.826 115 14 0 3162 3276 168181655 168181541 6.780000e-28 135.0
41 TraesCS2A01G432600 chr4B 77.725 211 22 15 3339 3527 649271862 649272069 5.320000e-19 106.0
42 TraesCS2A01G432600 chr5D 91.129 124 10 1 2475 2598 506244120 506243998 2.400000e-37 167.0
43 TraesCS2A01G432600 chr5B 92.727 110 8 0 2489 2598 637124139 637124030 4.020000e-35 159.0
44 TraesCS2A01G432600 chr5B 89.916 119 12 0 2479 2597 637019050 637018932 1.870000e-33 154.0
45 TraesCS2A01G432600 chr5B 86.111 108 15 0 2491 2598 636961759 636961652 2.460000e-22 117.0
46 TraesCS2A01G432600 chr5B 86.111 108 15 0 2491 2598 637114307 637114200 2.460000e-22 117.0
47 TraesCS2A01G432600 chr5B 86.111 108 15 0 2491 2598 637121013 637120906 2.460000e-22 117.0
48 TraesCS2A01G432600 chr5B 85.870 92 12 1 3435 3525 707404033 707404124 3.200000e-16 97.1
49 TraesCS2A01G432600 chr3B 85.246 122 18 0 3161 3282 533021665 533021544 4.080000e-25 126.0
50 TraesCS2A01G432600 chr3B 84.536 97 14 1 3430 3525 440082736 440082640 1.150000e-15 95.3
51 TraesCS2A01G432600 chr3D 85.124 121 17 1 3162 3282 456522919 456522800 5.280000e-24 122.0
52 TraesCS2A01G432600 chr4D 84.167 120 17 2 3161 3279 508338903 508339021 8.830000e-22 115.0
53 TraesCS2A01G432600 chr3A 87.234 94 12 0 3186 3279 544385761 544385854 1.480000e-19 108.0
54 TraesCS2A01G432600 chr4A 86.139 101 8 6 3338 3434 716802613 716802515 1.910000e-18 104.0
55 TraesCS2A01G432600 chr4A 84.848 99 9 6 3339 3433 19837205 19837301 1.150000e-15 95.3
56 TraesCS2A01G432600 chr1B 86.957 92 11 1 3435 3525 383783566 383783657 6.880000e-18 102.0
57 TraesCS2A01G432600 chr7B 86.170 94 12 1 3433 3525 299477906 299477813 2.470000e-17 100.0
58 TraesCS2A01G432600 chr7B 86.000 100 7 7 3339 3434 477377539 477377443 2.470000e-17 100.0
59 TraesCS2A01G432600 chr6B 85.000 100 9 6 3339 3435 645663862 645663958 3.200000e-16 97.1
60 TraesCS2A01G432600 chr6B 84.848 99 10 4 3339 3435 645886748 645886653 1.150000e-15 95.3
61 TraesCS2A01G432600 chr6B 83.838 99 15 1 3430 3527 88823454 88823356 4.140000e-15 93.5
62 TraesCS2A01G432600 chr6B 90.000 50 5 0 74 123 712617373 712617324 9.020000e-07 65.8
63 TraesCS2A01G432600 chr6B 100.000 33 0 0 75 107 500614597 500614629 1.170000e-05 62.1
64 TraesCS2A01G432600 chr7D 83.838 99 15 1 3430 3527 142421647 142421745 4.140000e-15 93.5
65 TraesCS2A01G432600 chr7D 89.583 48 5 0 74 121 615407593 615407640 1.170000e-05 62.1
66 TraesCS2A01G432600 chr1D 84.000 100 11 4 3339 3435 37879549 37879452 1.490000e-14 91.6
67 TraesCS2A01G432600 chr1D 100.000 34 0 0 74 107 279106032 279105999 3.240000e-06 63.9
68 TraesCS2A01G432600 chr6A 94.444 36 2 0 75 110 460301311 460301276 5.430000e-04 56.5


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G432600 chr2A 685749958 685753847 3889 True 7184.000000 7184 100.000000 1 3890 1 chr2A.!!$R3 3889
1 TraesCS2A01G432600 chr2A 660107864 660108937 1073 False 646.000000 791 91.519500 824 1947 2 chr2A.!!$F2 1123
2 TraesCS2A01G432600 chr2A 137270604 137271680 1076 True 464.166667 809 93.546667 824 1950 3 chr2A.!!$R4 1126
3 TraesCS2A01G432600 chr2D 543043235 543048184 4949 True 1958.000000 3476 90.470500 652 3117 2 chr2D.!!$R3 2465
4 TraesCS2A01G432600 chr2D 542945596 542946385 789 True 747.000000 747 84.060000 2332 3117 1 chr2D.!!$R1 785
5 TraesCS2A01G432600 chr2B 647740768 647744419 3651 True 1326.666667 2704 88.446000 74 3742 3 chr2B.!!$R3 3668
6 TraesCS2A01G432600 chr2B 647703546 647707145 3599 True 495.250000 1144 87.336500 2307 3847 4 chr2B.!!$R2 1540
7 TraesCS2A01G432600 chr6D 4872494 4873569 1075 True 476.500000 846 93.875333 824 1950 3 chr6D.!!$R2 1126
8 TraesCS2A01G432600 chr5A 12620334 12621407 1073 False 640.500000 780 90.649000 824 1947 2 chr5A.!!$F1 1123
9 TraesCS2A01G432600 chr5A 69011650 69012724 1074 True 448.300000 750 92.767667 824 1950 3 chr5A.!!$R1 1126
10 TraesCS2A01G432600 chr1A 310699970 310701043 1073 False 448.833333 769 93.202333 824 1947 3 chr1A.!!$F2 1123
11 TraesCS2A01G432600 chr4B 662856194 662857153 959 False 533.500000 619 89.135000 1015 2026 2 chr4B.!!$F2 1011

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
609 646 0.097150 GAAAACCCATTCGCTCGCTC 59.903 55.0 0.0 0.0 0.0 5.03 F
730 774 0.179001 AAGCCCGTATGCCATTACCC 60.179 55.0 0.0 0.0 0.0 3.69 F
1226 1275 0.749454 ATCCAATGTCCCTTGCTCGC 60.749 55.0 0.0 0.0 0.0 5.03 F
1300 1349 0.824109 GCTGATTAGGTTTTGGGGCC 59.176 55.0 0.0 0.0 0.0 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2242 2324 2.649190 TGCAAGTGGCTAAACAAGACA 58.351 42.857 0.00 0.0 42.71 3.41 R
2284 2370 2.821969 CAAGGATGGTTCAGGTTTCAGG 59.178 50.000 0.00 0.0 0.00 3.86 R
2748 2849 0.759346 ACAGGAAGTTGTTCGCCTCT 59.241 50.000 0.00 0.0 32.92 3.69 R
3150 3273 2.040278 AGGAGGCAGTACAAGATTTGCA 59.960 45.455 5.08 0.0 38.27 4.08 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.559655 TCAACAATGTCAAGTCAACTCCG 59.440 43.478 0.00 0.00 0.00 4.63
23 24 2.494059 ACAATGTCAAGTCAACTCCGG 58.506 47.619 0.00 0.00 0.00 5.14
24 25 2.158813 ACAATGTCAAGTCAACTCCGGT 60.159 45.455 0.00 0.00 0.00 5.28
25 26 3.070446 ACAATGTCAAGTCAACTCCGGTA 59.930 43.478 0.00 0.00 0.00 4.02
26 27 3.594603 ATGTCAAGTCAACTCCGGTAG 57.405 47.619 0.00 0.00 0.00 3.18
27 28 1.616865 TGTCAAGTCAACTCCGGTAGG 59.383 52.381 0.00 0.00 39.46 3.18
28 29 1.067071 GTCAAGTCAACTCCGGTAGGG 60.067 57.143 0.00 0.00 38.33 3.53
29 30 0.974383 CAAGTCAACTCCGGTAGGGT 59.026 55.000 0.00 0.00 38.33 4.34
30 31 2.173519 CAAGTCAACTCCGGTAGGGTA 58.826 52.381 0.00 0.00 38.33 3.69
31 32 2.140839 AGTCAACTCCGGTAGGGTAG 57.859 55.000 0.00 0.00 38.33 3.18
32 33 1.357079 AGTCAACTCCGGTAGGGTAGT 59.643 52.381 0.00 0.00 38.33 2.73
33 34 1.475682 GTCAACTCCGGTAGGGTAGTG 59.524 57.143 0.00 0.00 38.33 2.74
34 35 0.822164 CAACTCCGGTAGGGTAGTGG 59.178 60.000 0.00 0.00 38.33 4.00
35 36 0.974525 AACTCCGGTAGGGTAGTGGC 60.975 60.000 0.00 0.00 38.33 5.01
36 37 2.440796 TCCGGTAGGGTAGTGGCG 60.441 66.667 0.00 0.00 38.33 5.69
37 38 2.440796 CCGGTAGGGTAGTGGCGA 60.441 66.667 0.00 0.00 0.00 5.54
38 39 2.779033 CCGGTAGGGTAGTGGCGAC 61.779 68.421 0.00 0.00 0.00 5.19
39 40 2.048023 CGGTAGGGTAGTGGCGACA 61.048 63.158 0.45 0.00 38.70 4.35
40 41 1.597797 CGGTAGGGTAGTGGCGACAA 61.598 60.000 0.00 0.00 46.06 3.18
41 42 0.108472 GGTAGGGTAGTGGCGACAAC 60.108 60.000 0.00 0.00 46.06 3.32
42 43 0.457337 GTAGGGTAGTGGCGACAACG 60.457 60.000 0.00 0.00 46.06 4.10
43 44 0.608856 TAGGGTAGTGGCGACAACGA 60.609 55.000 0.00 0.00 46.06 3.85
57 58 4.936823 ACGACGCGTTGACGGCTT 62.937 61.111 32.39 6.34 39.56 4.35
58 59 4.409588 CGACGCGTTGACGGCTTG 62.410 66.667 22.24 0.00 39.56 4.01
59 60 3.335534 GACGCGTTGACGGCTTGT 61.336 61.111 15.53 0.00 38.32 3.16
60 61 2.877974 GACGCGTTGACGGCTTGTT 61.878 57.895 15.53 0.00 38.32 2.83
61 62 2.326550 CGCGTTGACGGCTTGTTT 59.673 55.556 0.00 0.00 40.23 2.83
62 63 1.298041 CGCGTTGACGGCTTGTTTT 60.298 52.632 0.00 0.00 40.23 2.43
63 64 1.528248 CGCGTTGACGGCTTGTTTTG 61.528 55.000 0.00 0.00 40.23 2.44
64 65 1.206115 GCGTTGACGGCTTGTTTTGG 61.206 55.000 5.62 0.00 40.23 3.28
65 66 0.099791 CGTTGACGGCTTGTTTTGGT 59.900 50.000 0.00 0.00 35.37 3.67
66 67 1.555477 GTTGACGGCTTGTTTTGGTG 58.445 50.000 0.00 0.00 0.00 4.17
67 68 1.135228 GTTGACGGCTTGTTTTGGTGT 60.135 47.619 0.00 0.00 0.00 4.16
68 69 0.736053 TGACGGCTTGTTTTGGTGTC 59.264 50.000 0.00 0.00 0.00 3.67
69 70 1.021968 GACGGCTTGTTTTGGTGTCT 58.978 50.000 0.00 0.00 0.00 3.41
70 71 0.738389 ACGGCTTGTTTTGGTGTCTG 59.262 50.000 0.00 0.00 0.00 3.51
71 72 0.738389 CGGCTTGTTTTGGTGTCTGT 59.262 50.000 0.00 0.00 0.00 3.41
72 73 1.944024 CGGCTTGTTTTGGTGTCTGTA 59.056 47.619 0.00 0.00 0.00 2.74
81 82 9.581099 CTTGTTTTGGTGTCTGTAGTAATTTTT 57.419 29.630 0.00 0.00 0.00 1.94
179 180 7.248437 GCAACTCGCTTTAATGGTTACTATTT 58.752 34.615 0.00 0.00 37.77 1.40
206 207 1.199615 TGCATCGTAGAACATCCCCA 58.800 50.000 0.00 0.00 43.58 4.96
227 228 5.121142 CCCATGTGCATTCAAATGAACTTTC 59.879 40.000 13.64 0.00 43.93 2.62
245 246 2.593346 TCGTTTGTGCCTGCAAAAAT 57.407 40.000 10.45 0.00 39.65 1.82
253 254 4.643463 TGTGCCTGCAAAAATCATCAATT 58.357 34.783 0.00 0.00 0.00 2.32
256 257 5.049267 GTGCCTGCAAAAATCATCAATTTGT 60.049 36.000 0.00 0.00 37.64 2.83
260 261 7.096394 GCCTGCAAAAATCATCAATTTGTTTTG 60.096 33.333 13.60 13.60 37.64 2.44
271 272 9.165035 TCATCAATTTGTTTTGCTCTTCTTTTT 57.835 25.926 0.00 0.00 0.00 1.94
354 356 4.028993 TGGTTCAAATCCAAGTACTCCC 57.971 45.455 0.00 0.00 31.50 4.30
356 358 4.262617 GGTTCAAATCCAAGTACTCCCTC 58.737 47.826 0.00 0.00 0.00 4.30
357 359 3.887621 TCAAATCCAAGTACTCCCTCG 57.112 47.619 0.00 0.00 0.00 4.63
363 400 3.350833 TCCAAGTACTCCCTCGAACTAC 58.649 50.000 0.00 0.00 0.00 2.73
370 407 2.701951 ACTCCCTCGAACTACCAAAACA 59.298 45.455 0.00 0.00 0.00 2.83
388 425 9.457436 ACCAAAACAACTTATATTTAGGATCGT 57.543 29.630 0.00 0.00 0.00 3.73
408 445 8.900781 GGATCGTAGGAAGTATACTATATTGCA 58.099 37.037 5.65 0.00 0.00 4.08
429 466 3.612472 AAAACATTGGTTACACCGACG 57.388 42.857 0.00 0.00 42.58 5.12
430 467 2.243602 AACATTGGTTACACCGACGT 57.756 45.000 0.00 0.00 42.58 4.34
432 469 0.711670 CATTGGTTACACCGACGTCG 59.288 55.000 30.33 30.33 42.58 5.12
445 482 4.747543 CGTCGGAAGTCGTCTCAG 57.252 61.111 0.00 0.00 40.32 3.35
446 483 1.512310 CGTCGGAAGTCGTCTCAGC 60.512 63.158 0.00 0.00 40.32 4.26
447 484 1.512310 GTCGGAAGTCGTCTCAGCG 60.512 63.158 0.00 0.00 40.32 5.18
448 485 2.202492 CGGAAGTCGTCTCAGCGG 60.202 66.667 0.00 0.00 0.00 5.52
449 486 2.507324 GGAAGTCGTCTCAGCGGC 60.507 66.667 0.00 0.00 36.64 6.53
450 487 2.876645 GAAGTCGTCTCAGCGGCG 60.877 66.667 0.51 0.51 41.85 6.46
451 488 3.324099 GAAGTCGTCTCAGCGGCGA 62.324 63.158 12.98 0.00 41.85 5.54
452 489 2.797866 GAAGTCGTCTCAGCGGCGAA 62.798 60.000 12.98 0.00 41.85 4.70
471 508 4.112634 CGAAGTCGAAATCTGCCTTCATA 58.887 43.478 9.49 0.00 43.02 2.15
493 530 4.652822 AGGCTAACAAAAGTTACTCCCTG 58.347 43.478 0.00 0.00 0.00 4.45
502 539 7.215085 ACAAAAGTTACTCCCTGTGTAAGTAG 58.785 38.462 0.00 0.00 33.83 2.57
503 540 6.990908 AAAGTTACTCCCTGTGTAAGTAGT 57.009 37.500 0.00 0.00 33.83 2.73
513 550 8.654485 TCCCTGTGTAAGTAGTTATCTAAACA 57.346 34.615 0.00 0.00 0.00 2.83
548 585 3.806949 TTTATGAAGGGAGTGCAGGTT 57.193 42.857 0.00 0.00 0.00 3.50
556 593 3.910989 AGGGAGTGCAGGTTTAGTTTTT 58.089 40.909 0.00 0.00 0.00 1.94
581 618 1.535444 TTTCCTCCCCAGTCGCTCA 60.535 57.895 0.00 0.00 0.00 4.26
588 625 0.608640 CCCCAGTCGCTCAAAGTACT 59.391 55.000 0.00 0.00 0.00 2.73
589 626 1.673033 CCCCAGTCGCTCAAAGTACTG 60.673 57.143 0.00 0.00 39.22 2.74
609 646 0.097150 GAAAACCCATTCGCTCGCTC 59.903 55.000 0.00 0.00 0.00 5.03
612 649 0.741221 AACCCATTCGCTCGCTCTTC 60.741 55.000 0.00 0.00 0.00 2.87
617 654 2.133553 CATTCGCTCGCTCTTCATCAT 58.866 47.619 0.00 0.00 0.00 2.45
618 655 1.845266 TTCGCTCGCTCTTCATCATC 58.155 50.000 0.00 0.00 0.00 2.92
619 656 0.740737 TCGCTCGCTCTTCATCATCA 59.259 50.000 0.00 0.00 0.00 3.07
621 658 1.720316 CGCTCGCTCTTCATCATCATC 59.280 52.381 0.00 0.00 0.00 2.92
622 659 2.752121 GCTCGCTCTTCATCATCATCA 58.248 47.619 0.00 0.00 0.00 3.07
624 661 3.184783 GCTCGCTCTTCATCATCATCAAG 59.815 47.826 0.00 0.00 0.00 3.02
625 662 4.370049 CTCGCTCTTCATCATCATCAAGT 58.630 43.478 0.00 0.00 0.00 3.16
626 663 4.117685 TCGCTCTTCATCATCATCAAGTG 58.882 43.478 0.00 0.00 0.00 3.16
627 664 3.247886 CGCTCTTCATCATCATCAAGTGG 59.752 47.826 0.00 0.00 0.00 4.00
628 665 4.449131 GCTCTTCATCATCATCAAGTGGA 58.551 43.478 0.00 0.00 0.00 4.02
629 666 4.880120 GCTCTTCATCATCATCAAGTGGAA 59.120 41.667 0.00 0.00 0.00 3.53
630 667 5.356190 GCTCTTCATCATCATCAAGTGGAAA 59.644 40.000 0.00 0.00 0.00 3.13
631 668 6.127814 GCTCTTCATCATCATCAAGTGGAAAA 60.128 38.462 0.00 0.00 0.00 2.29
632 669 7.576287 GCTCTTCATCATCATCAAGTGGAAAAA 60.576 37.037 0.00 0.00 0.00 1.94
730 774 0.179001 AAGCCCGTATGCCATTACCC 60.179 55.000 0.00 0.00 0.00 3.69
741 785 3.103213 ATTACCCGGGCCCTGCAT 61.103 61.111 24.08 6.83 0.00 3.96
763 807 1.221566 CCATCTCCATCCACGTGCA 59.778 57.895 10.91 0.00 0.00 4.57
813 858 2.124695 CCCGAACCCTAGCAAGCC 60.125 66.667 0.00 0.00 0.00 4.35
822 867 0.967380 CCTAGCAAGCCAAACCCCTG 60.967 60.000 0.00 0.00 0.00 4.45
977 1025 2.894126 TCGATCTAAGCCTGAAGGATCC 59.106 50.000 2.48 2.48 37.39 3.36
980 1028 2.467880 TCTAAGCCTGAAGGATCCGTT 58.532 47.619 5.98 0.79 37.39 4.44
986 1034 2.076863 CCTGAAGGATCCGTTGTTGAC 58.923 52.381 5.98 0.00 37.39 3.18
1190 1239 2.107953 GGCTCAGGTCAGATCGCC 59.892 66.667 0.00 0.00 0.00 5.54
1197 1246 2.663188 GTCAGATCGCCGCCCATC 60.663 66.667 0.00 0.00 0.00 3.51
1226 1275 0.749454 ATCCAATGTCCCTTGCTCGC 60.749 55.000 0.00 0.00 0.00 5.03
1248 1297 3.453424 TCGTGGATGTGGATTGTATTCG 58.547 45.455 0.00 0.00 0.00 3.34
1300 1349 0.824109 GCTGATTAGGTTTTGGGGCC 59.176 55.000 0.00 0.00 0.00 5.80
1333 1383 5.803461 TCGAATTTGGACTGTATCAACTACG 59.197 40.000 0.00 0.00 32.61 3.51
1349 1399 5.570206 TCAACTACGTATGCTTTACTTGTCG 59.430 40.000 0.00 0.00 0.00 4.35
1357 1407 1.334054 CTTTACTTGTCGTCGGTCGG 58.666 55.000 0.00 0.00 40.32 4.79
1469 1520 3.119291 CTGCGAGTCAACTGATATCCAC 58.881 50.000 0.00 0.00 0.00 4.02
1477 1528 7.117379 CGAGTCAACTGATATCCACGTATAGTA 59.883 40.741 0.00 0.00 0.00 1.82
1485 1536 8.037382 TGATATCCACGTATAGTAGTGTTAGC 57.963 38.462 0.00 0.00 36.69 3.09
1611 1687 4.898328 ATAAACGTGCTCAGTAACGAAC 57.102 40.909 8.78 0.00 42.32 3.95
1622 1698 4.923893 TCAGTAACGAACGAAAACTCTGA 58.076 39.130 0.14 0.00 0.00 3.27
1624 1700 5.401376 TCAGTAACGAACGAAAACTCTGATG 59.599 40.000 0.14 0.00 0.00 3.07
1625 1701 4.684703 AGTAACGAACGAAAACTCTGATGG 59.315 41.667 0.14 0.00 0.00 3.51
1626 1702 3.380479 ACGAACGAAAACTCTGATGGA 57.620 42.857 0.14 0.00 0.00 3.41
1627 1703 3.318017 ACGAACGAAAACTCTGATGGAG 58.682 45.455 0.14 0.00 46.87 3.86
1947 2024 4.637483 ATTATTTGGTCCTGTGAATGCG 57.363 40.909 0.00 0.00 0.00 4.73
2105 2182 2.102757 TGTTGCTTACGGGTCTGTTACA 59.897 45.455 0.00 0.00 0.00 2.41
2227 2309 9.110502 CACTGTGTTATCTACTGTCTACTATGA 57.889 37.037 0.00 0.00 0.00 2.15
2242 2324 8.531982 TGTCTACTATGACATTTTACTGCTTCT 58.468 33.333 0.00 0.00 41.43 2.85
2284 2370 7.738345 TGCAAAGTCTTTTGAAAAAGTTTAGC 58.262 30.769 13.68 12.53 45.21 3.09
2346 2432 6.095440 AGCAATTATGTTAGTTTAGCTGGTGG 59.905 38.462 0.00 0.00 0.00 4.61
2359 2445 2.035832 AGCTGGTGGTGTTAAATGTTGC 59.964 45.455 0.00 0.00 0.00 4.17
2424 2512 7.528996 TCAACCAAGATTTCAAGTGATCAAT 57.471 32.000 0.00 0.00 0.00 2.57
2589 2678 4.339247 CCTCTGACCAACAACAAAGTCATT 59.661 41.667 0.00 0.00 38.49 2.57
2748 2849 1.388065 CCGTTGGCCCACACTTCAAA 61.388 55.000 7.86 0.00 0.00 2.69
2896 2997 7.386851 TGTTAGAAGGATGAACTAGGTTGAAG 58.613 38.462 0.00 0.00 0.00 3.02
3140 3263 3.756082 AGTTCCTTGCCATATTTGGGA 57.244 42.857 4.23 0.00 43.84 4.37
3143 3266 5.969086 AGTTCCTTGCCATATTTGGGATAT 58.031 37.500 4.23 0.00 43.66 1.63
3150 3273 5.841209 TGCCATATTTGGGATATTAGGCAT 58.159 37.500 4.23 0.00 43.93 4.40
3165 3288 5.565592 TTAGGCATGCAAATCTTGTACTG 57.434 39.130 21.36 0.00 0.00 2.74
3222 3382 7.544217 ACTTTTCTTGTTTTAATCGCACAACTT 59.456 29.630 0.00 0.00 0.00 2.66
3223 3383 7.444558 TTTCTTGTTTTAATCGCACAACTTC 57.555 32.000 0.00 0.00 0.00 3.01
3228 3388 5.741510 TGTTTTAATCGCACAACTTCAACTG 59.258 36.000 0.00 0.00 0.00 3.16
3232 3392 0.732571 CGCACAACTTCAACTGTGGT 59.267 50.000 4.53 0.00 42.62 4.16
3299 3459 2.076100 CAAAGCGGATGTGCTGTTCTA 58.924 47.619 0.00 0.00 46.60 2.10
3317 3477 7.413438 GCTGTTCTACAAGGATGTTATCAGTTG 60.413 40.741 0.00 0.00 41.05 3.16
3330 3490 9.494479 GATGTTATCAGTTGTACATGTTCAATG 57.506 33.333 19.14 16.76 31.76 2.82
3340 3500 2.988493 ACATGTTCAATGCGTGCATTTC 59.012 40.909 16.93 11.05 43.32 2.17
3341 3501 2.063156 TGTTCAATGCGTGCATTTCC 57.937 45.000 16.93 8.68 43.32 3.13
3343 3503 2.035704 TGTTCAATGCGTGCATTTCCTT 59.964 40.909 16.93 0.00 43.32 3.36
3344 3504 2.350899 TCAATGCGTGCATTTCCTTG 57.649 45.000 16.93 7.92 43.32 3.61
3408 3582 9.569122 AAATAGAAGGTGTATTGTGTAAACACT 57.431 29.630 13.95 0.00 46.55 3.55
3411 3585 7.280356 AGAAGGTGTATTGTGTAAACACTCTT 58.720 34.615 13.95 6.55 46.55 2.85
3412 3586 7.773690 AGAAGGTGTATTGTGTAAACACTCTTT 59.226 33.333 13.95 0.30 46.55 2.52
3414 3588 7.703328 AGGTGTATTGTGTAAACACTCTTTTG 58.297 34.615 13.95 0.00 46.55 2.44
3418 3595 8.564574 TGTATTGTGTAAACACTCTTTTGGATC 58.435 33.333 13.95 0.00 46.55 3.36
3420 3597 7.639113 TTGTGTAAACACTCTTTTGGATCTT 57.361 32.000 13.95 0.00 46.55 2.40
3441 3618 4.882842 TTTTTAGGGATTTGAGGCAACC 57.117 40.909 0.00 0.00 37.17 3.77
3481 3677 6.371548 TGTCAATTAGTCAGGTGTAATCTTGC 59.628 38.462 0.00 0.00 0.00 4.01
3482 3678 5.880332 TCAATTAGTCAGGTGTAATCTTGCC 59.120 40.000 0.00 0.00 0.00 4.52
3488 3684 4.220602 GTCAGGTGTAATCTTGCCCAAAAT 59.779 41.667 0.00 0.00 0.00 1.82
3491 3687 6.495181 TCAGGTGTAATCTTGCCCAAAATTTA 59.505 34.615 0.00 0.00 0.00 1.40
3497 3693 9.956640 TGTAATCTTGCCCAAAATTTATGAAAT 57.043 25.926 0.00 0.00 0.00 2.17
3513 3709 3.987547 TGAAATTTTTCCTTCATGCGCA 58.012 36.364 14.96 14.96 36.36 6.09
3516 3712 5.120519 TGAAATTTTTCCTTCATGCGCATTC 59.879 36.000 22.81 12.21 36.36 2.67
3517 3713 2.652941 TTTTCCTTCATGCGCATTCC 57.347 45.000 22.81 0.00 0.00 3.01
3525 3721 5.105392 TCCTTCATGCGCATTCCTTAATTTT 60.105 36.000 22.81 0.00 0.00 1.82
3526 3722 5.581874 CCTTCATGCGCATTCCTTAATTTTT 59.418 36.000 22.81 0.00 0.00 1.94
3527 3723 6.237915 CCTTCATGCGCATTCCTTAATTTTTC 60.238 38.462 22.81 0.00 0.00 2.29
3528 3724 5.718146 TCATGCGCATTCCTTAATTTTTCA 58.282 33.333 22.81 0.00 0.00 2.69
3529 3725 6.162079 TCATGCGCATTCCTTAATTTTTCAA 58.838 32.000 22.81 0.00 0.00 2.69
3531 3727 6.645700 TGCGCATTCCTTAATTTTTCAATC 57.354 33.333 5.66 0.00 0.00 2.67
3532 3728 5.288232 TGCGCATTCCTTAATTTTTCAATCG 59.712 36.000 5.66 0.00 0.00 3.34
3533 3729 5.288472 GCGCATTCCTTAATTTTTCAATCGT 59.712 36.000 0.30 0.00 0.00 3.73
3534 3730 6.183360 GCGCATTCCTTAATTTTTCAATCGTT 60.183 34.615 0.30 0.00 0.00 3.85
3535 3731 7.383361 CGCATTCCTTAATTTTTCAATCGTTC 58.617 34.615 0.00 0.00 0.00 3.95
3536 3732 7.383361 GCATTCCTTAATTTTTCAATCGTTCG 58.617 34.615 0.00 0.00 0.00 3.95
3537 3733 7.061789 GCATTCCTTAATTTTTCAATCGTTCGT 59.938 33.333 0.00 0.00 0.00 3.85
3539 3735 8.496872 TTCCTTAATTTTTCAATCGTTCGTTC 57.503 30.769 0.00 0.00 0.00 3.95
3540 3736 7.640852 TCCTTAATTTTTCAATCGTTCGTTCA 58.359 30.769 0.00 0.00 0.00 3.18
3541 3737 7.801315 TCCTTAATTTTTCAATCGTTCGTTCAG 59.199 33.333 0.00 0.00 0.00 3.02
3550 3763 0.246635 CGTTCGTTCAGTGGAGGGAT 59.753 55.000 0.00 0.00 0.00 3.85
3566 3779 5.166398 GGAGGGATTATGTATTAACGGTCG 58.834 45.833 0.00 0.00 0.00 4.79
3572 3786 5.954434 TTATGTATTAACGGTCGAGTTGC 57.046 39.130 0.59 0.00 35.70 4.17
3577 3791 1.348538 TAACGGTCGAGTTGCGCATG 61.349 55.000 12.75 1.43 40.61 4.06
3586 3800 2.815211 TTGCGCATGAGAGACCGC 60.815 61.111 12.75 3.19 45.99 5.68
3628 3862 4.938226 GGGAGTATCACTTTCAACTTCCAG 59.062 45.833 0.00 0.00 37.53 3.86
3650 3884 3.440522 GTCTTTGGCGCTAATTTCCTCTT 59.559 43.478 7.14 0.00 0.00 2.85
3724 3970 3.813166 AGTGTGTATACAAGCGCAAAAGT 59.187 39.130 11.47 4.60 38.82 2.66
3770 4018 4.074970 GAGCCAGAACTCCATTCAAGAAA 58.925 43.478 0.00 0.00 40.09 2.52
3773 4021 3.192212 CCAGAACTCCATTCAAGAAAGCC 59.808 47.826 0.00 0.00 40.09 4.35
3777 4025 1.475682 CTCCATTCAAGAAAGCCCTGC 59.524 52.381 0.00 0.00 0.00 4.85
3784 4032 0.251077 AAGAAAGCCCTGCTCCACAG 60.251 55.000 0.00 0.00 46.77 3.66
3798 4046 0.886490 CCACAGGCGCAGAAGAAAGT 60.886 55.000 10.83 0.00 0.00 2.66
3800 4048 0.947244 ACAGGCGCAGAAGAAAGTTG 59.053 50.000 10.83 0.00 0.00 3.16
3806 4054 2.378806 CGCAGAAGAAAGTTGTTGCTG 58.621 47.619 0.00 0.00 0.00 4.41
3814 4062 5.491635 AGAAAGTTGTTGCTGTTCTTCTC 57.508 39.130 0.00 0.00 0.00 2.87
3820 4068 0.603707 TTGCTGTTCTTCTCGGGCAG 60.604 55.000 0.00 0.00 0.00 4.85
3825 4073 0.108567 GTTCTTCTCGGGCAGAGGAC 60.109 60.000 14.68 5.45 46.82 3.85
3847 4098 1.079819 CATCTCGAGTGCGGGTTGT 60.080 57.895 13.13 0.00 39.57 3.32
3848 4099 1.079819 ATCTCGAGTGCGGGTTGTG 60.080 57.895 13.13 0.00 39.57 3.33
3849 4100 3.414700 CTCGAGTGCGGGTTGTGC 61.415 66.667 3.62 0.00 38.28 4.57
3850 4101 4.228567 TCGAGTGCGGGTTGTGCA 62.229 61.111 0.00 0.00 40.70 4.57
3851 4102 3.716006 CGAGTGCGGGTTGTGCAG 61.716 66.667 0.00 0.00 44.21 4.41
3852 4103 4.030452 GAGTGCGGGTTGTGCAGC 62.030 66.667 0.00 0.00 44.21 5.25
3857 4108 4.263209 CGGGTTGTGCAGCGCAAA 62.263 61.111 22.83 4.92 41.47 3.68
3858 4109 2.658268 GGGTTGTGCAGCGCAAAC 60.658 61.111 25.88 25.88 41.47 2.93
3859 4110 2.103934 GGTTGTGCAGCGCAAACA 59.896 55.556 28.25 8.07 40.74 2.83
3860 4111 1.518133 GGTTGTGCAGCGCAAACAA 60.518 52.632 28.25 14.20 40.74 2.83
3865 4116 0.503961 GTGCAGCGCAAACAATTGTC 59.496 50.000 12.39 0.00 41.47 3.18
3869 4120 2.371923 GCGCAAACAATTGTCGCCC 61.372 57.895 24.70 14.31 46.54 6.13
3876 4127 2.359478 AATTGTCGCCCACCGGTC 60.359 61.111 2.59 0.00 37.59 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.303990 CCGGAGTTGACTTGACATTGTTG 60.304 47.826 0.00 0.00 0.00 3.33
3 4 2.158813 ACCGGAGTTGACTTGACATTGT 60.159 45.455 9.46 0.00 0.00 2.71
4 5 2.494059 ACCGGAGTTGACTTGACATTG 58.506 47.619 9.46 0.00 0.00 2.82
5 6 2.930826 ACCGGAGTTGACTTGACATT 57.069 45.000 9.46 0.00 0.00 2.71
6 7 2.233922 CCTACCGGAGTTGACTTGACAT 59.766 50.000 9.46 0.00 0.00 3.06
7 8 1.616865 CCTACCGGAGTTGACTTGACA 59.383 52.381 9.46 0.00 0.00 3.58
8 9 1.067071 CCCTACCGGAGTTGACTTGAC 60.067 57.143 9.46 0.00 0.00 3.18
9 10 1.263356 CCCTACCGGAGTTGACTTGA 58.737 55.000 9.46 0.00 0.00 3.02
10 11 0.974383 ACCCTACCGGAGTTGACTTG 59.026 55.000 9.46 0.00 34.64 3.16
11 12 2.225217 ACTACCCTACCGGAGTTGACTT 60.225 50.000 9.46 0.00 34.64 3.01
12 13 1.357079 ACTACCCTACCGGAGTTGACT 59.643 52.381 9.46 0.00 34.64 3.41
13 14 1.475682 CACTACCCTACCGGAGTTGAC 59.524 57.143 9.46 0.00 34.64 3.18
14 15 1.617804 CCACTACCCTACCGGAGTTGA 60.618 57.143 9.46 0.00 34.64 3.18
15 16 0.822164 CCACTACCCTACCGGAGTTG 59.178 60.000 9.46 3.51 34.64 3.16
16 17 0.974525 GCCACTACCCTACCGGAGTT 60.975 60.000 9.46 0.00 34.64 3.01
17 18 1.380920 GCCACTACCCTACCGGAGT 60.381 63.158 9.46 0.00 34.64 3.85
18 19 2.487532 CGCCACTACCCTACCGGAG 61.488 68.421 9.46 0.28 34.64 4.63
19 20 2.440796 CGCCACTACCCTACCGGA 60.441 66.667 9.46 0.00 34.64 5.14
20 21 2.440796 TCGCCACTACCCTACCGG 60.441 66.667 0.00 0.00 37.81 5.28
21 22 1.597797 TTGTCGCCACTACCCTACCG 61.598 60.000 0.00 0.00 0.00 4.02
22 23 0.108472 GTTGTCGCCACTACCCTACC 60.108 60.000 0.00 0.00 0.00 3.18
23 24 0.457337 CGTTGTCGCCACTACCCTAC 60.457 60.000 0.00 0.00 0.00 3.18
24 25 0.608856 TCGTTGTCGCCACTACCCTA 60.609 55.000 0.00 0.00 36.96 3.53
25 26 1.904865 TCGTTGTCGCCACTACCCT 60.905 57.895 0.00 0.00 36.96 4.34
26 27 1.735559 GTCGTTGTCGCCACTACCC 60.736 63.158 0.00 0.00 36.96 3.69
27 28 2.084681 CGTCGTTGTCGCCACTACC 61.085 63.158 0.00 0.00 36.96 3.18
28 29 2.713894 GCGTCGTTGTCGCCACTAC 61.714 63.158 0.00 0.00 46.61 2.73
29 30 2.429571 GCGTCGTTGTCGCCACTA 60.430 61.111 0.00 0.00 46.61 2.74
40 41 4.936823 AAGCCGTCAACGCGTCGT 62.937 61.111 14.44 0.00 43.97 4.34
41 42 4.409588 CAAGCCGTCAACGCGTCG 62.410 66.667 14.44 12.62 38.18 5.12
42 43 2.369477 AAACAAGCCGTCAACGCGTC 62.369 55.000 14.44 0.00 38.18 5.19
43 44 1.984321 AAAACAAGCCGTCAACGCGT 61.984 50.000 5.58 5.58 38.18 6.01
44 45 1.298041 AAAACAAGCCGTCAACGCG 60.298 52.632 3.53 3.53 38.18 6.01
45 46 1.206115 CCAAAACAAGCCGTCAACGC 61.206 55.000 0.00 0.00 38.18 4.84
46 47 0.099791 ACCAAAACAAGCCGTCAACG 59.900 50.000 0.00 0.00 39.44 4.10
47 48 1.135228 ACACCAAAACAAGCCGTCAAC 60.135 47.619 0.00 0.00 0.00 3.18
48 49 1.133407 GACACCAAAACAAGCCGTCAA 59.867 47.619 0.00 0.00 0.00 3.18
49 50 0.736053 GACACCAAAACAAGCCGTCA 59.264 50.000 0.00 0.00 0.00 4.35
50 51 1.021968 AGACACCAAAACAAGCCGTC 58.978 50.000 0.00 0.00 0.00 4.79
51 52 0.738389 CAGACACCAAAACAAGCCGT 59.262 50.000 0.00 0.00 0.00 5.68
52 53 0.738389 ACAGACACCAAAACAAGCCG 59.262 50.000 0.00 0.00 0.00 5.52
53 54 2.949644 ACTACAGACACCAAAACAAGCC 59.050 45.455 0.00 0.00 0.00 4.35
54 55 5.744666 TTACTACAGACACCAAAACAAGC 57.255 39.130 0.00 0.00 0.00 4.01
55 56 9.581099 AAAAATTACTACAGACACCAAAACAAG 57.419 29.630 0.00 0.00 0.00 3.16
90 91 9.502091 AGTTTATCACAAGTACAAAGCATCTTA 57.498 29.630 0.00 0.00 0.00 2.10
91 92 8.396272 AGTTTATCACAAGTACAAAGCATCTT 57.604 30.769 0.00 0.00 0.00 2.40
123 124 8.570068 AAGGTTTCCATAATTCGCTAAAGTAA 57.430 30.769 0.00 0.00 0.00 2.24
128 129 7.455641 TTGAAAGGTTTCCATAATTCGCTAA 57.544 32.000 0.05 0.00 36.36 3.09
132 133 6.155827 TGCTTTGAAAGGTTTCCATAATTCG 58.844 36.000 7.09 0.00 36.36 3.34
179 180 6.183360 GGGATGTTCTACGATGCATTTTGTAA 60.183 38.462 0.00 0.00 0.00 2.41
188 189 2.146342 CATGGGGATGTTCTACGATGC 58.854 52.381 0.00 0.00 0.00 3.91
206 207 5.531634 ACGAAAGTTCATTTGAATGCACAT 58.468 33.333 8.73 0.00 46.40 3.21
227 228 2.200067 TGATTTTTGCAGGCACAAACG 58.800 42.857 7.65 0.00 39.18 3.60
236 237 7.646130 AGCAAAACAAATTGATGATTTTTGCAG 59.354 29.630 28.63 7.72 44.15 4.41
245 246 8.721019 AAAAGAAGAGCAAAACAAATTGATGA 57.279 26.923 0.00 0.00 31.84 2.92
316 317 3.182887 ACCATTTGAATGCAACCCCTA 57.817 42.857 0.00 0.00 35.08 3.53
324 326 5.702209 ACTTGGATTTGAACCATTTGAATGC 59.298 36.000 0.00 0.00 37.26 3.56
429 466 1.512310 CGCTGAGACGACTTCCGAC 60.512 63.158 0.00 0.00 41.76 4.79
430 467 2.687805 CCGCTGAGACGACTTCCGA 61.688 63.158 0.00 0.00 41.76 4.55
432 469 2.507324 GCCGCTGAGACGACTTCC 60.507 66.667 0.00 0.00 34.06 3.46
438 475 2.876645 GACTTCGCCGCTGAGACG 60.877 66.667 0.00 0.00 0.00 4.18
439 476 2.797866 TTCGACTTCGCCGCTGAGAC 62.798 60.000 0.00 0.00 39.60 3.36
440 477 2.137425 TTTCGACTTCGCCGCTGAGA 62.137 55.000 0.00 0.00 39.60 3.27
441 478 1.078759 ATTTCGACTTCGCCGCTGAG 61.079 55.000 0.00 0.00 39.60 3.35
442 479 1.076533 GATTTCGACTTCGCCGCTGA 61.077 55.000 0.00 0.00 39.60 4.26
443 480 1.078759 AGATTTCGACTTCGCCGCTG 61.079 55.000 0.00 0.00 39.60 5.18
444 481 1.078759 CAGATTTCGACTTCGCCGCT 61.079 55.000 0.00 0.00 39.60 5.52
445 482 1.345176 CAGATTTCGACTTCGCCGC 59.655 57.895 0.00 0.00 39.60 6.53
446 483 1.345176 GCAGATTTCGACTTCGCCG 59.655 57.895 0.00 0.00 39.60 6.46
447 484 0.741221 AGGCAGATTTCGACTTCGCC 60.741 55.000 15.53 15.53 39.60 5.54
448 485 1.061276 GAAGGCAGATTTCGACTTCGC 59.939 52.381 0.00 0.00 39.60 4.70
449 486 2.337583 TGAAGGCAGATTTCGACTTCG 58.662 47.619 1.60 0.00 40.18 3.79
450 487 4.509600 CCTATGAAGGCAGATTTCGACTTC 59.490 45.833 0.00 0.00 35.64 3.01
451 488 4.446371 CCTATGAAGGCAGATTTCGACTT 58.554 43.478 0.00 0.00 35.64 3.01
452 489 4.065321 CCTATGAAGGCAGATTTCGACT 57.935 45.455 0.00 0.00 35.64 4.18
471 508 4.104261 ACAGGGAGTAACTTTTGTTAGCCT 59.896 41.667 0.00 0.00 44.56 4.58
527 564 3.806949 ACCTGCACTCCCTTCATAAAA 57.193 42.857 0.00 0.00 0.00 1.52
529 566 3.806949 AAACCTGCACTCCCTTCATAA 57.193 42.857 0.00 0.00 0.00 1.90
530 567 3.844211 ACTAAACCTGCACTCCCTTCATA 59.156 43.478 0.00 0.00 0.00 2.15
531 568 2.644798 ACTAAACCTGCACTCCCTTCAT 59.355 45.455 0.00 0.00 0.00 2.57
532 569 2.054799 ACTAAACCTGCACTCCCTTCA 58.945 47.619 0.00 0.00 0.00 3.02
533 570 2.861147 ACTAAACCTGCACTCCCTTC 57.139 50.000 0.00 0.00 0.00 3.46
534 571 3.595190 AAACTAAACCTGCACTCCCTT 57.405 42.857 0.00 0.00 0.00 3.95
535 572 3.595190 AAAACTAAACCTGCACTCCCT 57.405 42.857 0.00 0.00 0.00 4.20
563 600 1.125093 TTGAGCGACTGGGGAGGAAA 61.125 55.000 0.00 0.00 0.00 3.13
574 611 3.059120 GGTTTTCCAGTACTTTGAGCGAC 60.059 47.826 0.00 0.00 40.31 5.19
589 626 1.136774 GCGAGCGAATGGGTTTTCC 59.863 57.895 0.00 0.00 39.75 3.13
656 693 9.040939 GCAGTTGTTACCAAATATTTTGTTCTT 57.959 29.630 9.92 0.00 30.94 2.52
680 724 2.494530 GGCCCCTGTTTCGTTTGCA 61.495 57.895 0.00 0.00 0.00 4.08
709 753 2.028876 GGTAATGGCATACGGGCTTTT 58.971 47.619 0.00 0.00 43.83 2.27
741 785 0.031515 ACGTGGATGGAGATGGGGTA 60.032 55.000 0.00 0.00 0.00 3.69
744 788 1.524621 GCACGTGGATGGAGATGGG 60.525 63.158 18.88 0.00 0.00 4.00
763 807 1.738099 GTCGCGAGTGGCTTGATGT 60.738 57.895 10.24 0.00 40.44 3.06
813 858 2.943033 CGGATTAAGTAGCAGGGGTTTG 59.057 50.000 0.00 0.00 0.00 2.93
822 867 0.853419 GAGTGCGCGGATTAAGTAGC 59.147 55.000 8.83 0.00 0.00 3.58
953 1001 3.632333 TCCTTCAGGCTTAGATCGAGAA 58.368 45.455 3.66 0.00 34.44 2.87
1190 1239 2.794627 GATCGAGCGAGAGATGGGCG 62.795 65.000 0.00 0.00 0.00 6.13
1197 1246 1.601663 GGACATTGGATCGAGCGAGAG 60.602 57.143 0.00 0.00 0.00 3.20
1226 1275 3.490896 CGAATACAATCCACATCCACGAG 59.509 47.826 0.00 0.00 0.00 4.18
1281 1330 0.824109 GGCCCCAAAACCTAATCAGC 59.176 55.000 0.00 0.00 0.00 4.26
1300 1349 0.871722 TCCAAATTCGACTTGGCACG 59.128 50.000 17.21 0.00 42.68 5.34
1333 1383 3.248266 ACCGACGACAAGTAAAGCATAC 58.752 45.455 0.00 0.00 0.00 2.39
1349 1399 0.108472 CCTTTTCCCTACCGACCGAC 60.108 60.000 0.00 0.00 0.00 4.79
1357 1407 2.764572 TCCGATCACTCCTTTTCCCTAC 59.235 50.000 0.00 0.00 0.00 3.18
1469 1520 8.900511 TTAAACACAGCTAACACTACTATACG 57.099 34.615 0.00 0.00 0.00 3.06
1477 1528 6.770785 TGAAGGAATTAAACACAGCTAACACT 59.229 34.615 0.00 0.00 0.00 3.55
1485 1536 8.103948 ACTGAATCTGAAGGAATTAAACACAG 57.896 34.615 0.00 0.00 0.00 3.66
1518 1569 7.063593 AGCTAGATTAGATGTTGGACTACAGA 58.936 38.462 0.00 0.00 0.00 3.41
1624 1700 6.070194 ACCCACATTAGCATATATGGTACTCC 60.070 42.308 21.32 1.43 40.12 3.85
1625 1701 6.818644 CACCCACATTAGCATATATGGTACTC 59.181 42.308 21.32 2.11 40.12 2.59
1626 1702 6.272324 ACACCCACATTAGCATATATGGTACT 59.728 38.462 21.32 14.81 40.12 2.73
1627 1703 6.472887 ACACCCACATTAGCATATATGGTAC 58.527 40.000 21.32 2.80 40.12 3.34
1633 1709 5.995446 TCACAACACCCACATTAGCATATA 58.005 37.500 0.00 0.00 0.00 0.86
1947 2024 5.998454 AGTAGATGTATCAAGCAACATGC 57.002 39.130 0.00 0.00 45.46 4.06
1990 2067 9.772973 TCTGTAGAAGTAAATTTTAGCAGTGAA 57.227 29.630 0.00 0.00 0.00 3.18
2105 2182 9.793259 TCAATTAAGACTCAAAAAGGTAGACAT 57.207 29.630 0.00 0.00 0.00 3.06
2227 2309 6.699575 AACAAGACAGAAGCAGTAAAATGT 57.300 33.333 0.00 0.00 0.00 2.71
2242 2324 2.649190 TGCAAGTGGCTAAACAAGACA 58.351 42.857 0.00 0.00 42.71 3.41
2284 2370 2.821969 CAAGGATGGTTCAGGTTTCAGG 59.178 50.000 0.00 0.00 0.00 3.86
2346 2432 9.769093 CCTATAGTTTGTAGCAACATTTAACAC 57.231 33.333 0.00 0.00 34.97 3.32
2424 2512 9.996554 TCATAACAAGTTTCTAGTTCATCTGAA 57.003 29.630 0.00 0.00 0.00 3.02
2565 2654 3.054728 TGACTTTGTTGTTGGTCAGAGGA 60.055 43.478 0.00 0.00 34.38 3.71
2589 2678 3.951680 GGTTGAAGAAACAAACCTCCTCA 59.048 43.478 0.00 0.00 40.86 3.86
2748 2849 0.759346 ACAGGAAGTTGTTCGCCTCT 59.241 50.000 0.00 0.00 32.92 3.69
2896 2997 3.648545 ACAGGGTATTATCAAGGAGCTCC 59.351 47.826 26.22 26.22 0.00 4.70
3140 3263 7.522725 GCAGTACAAGATTTGCATGCCTAATAT 60.523 37.037 16.68 9.43 36.59 1.28
3143 3266 4.142403 GCAGTACAAGATTTGCATGCCTAA 60.142 41.667 16.68 10.06 36.59 2.69
3150 3273 2.040278 AGGAGGCAGTACAAGATTTGCA 59.960 45.455 5.08 0.00 38.27 4.08
3165 3288 3.653352 ACCTTATATCTTGGGAAGGAGGC 59.347 47.826 6.52 0.00 40.88 4.70
3228 3388 7.040686 AGTGGACATACAATAAGTGAAAACCAC 60.041 37.037 0.00 0.00 46.03 4.16
3288 3448 3.769739 ACATCCTTGTAGAACAGCACA 57.230 42.857 0.00 0.00 33.16 4.57
3299 3459 7.168219 ACATGTACAACTGATAACATCCTTGT 58.832 34.615 0.00 0.00 37.82 3.16
3317 3477 2.610219 TGCACGCATTGAACATGTAC 57.390 45.000 0.00 0.00 0.00 2.90
3330 3490 4.275936 ACCTTATATCAAGGAAATGCACGC 59.724 41.667 9.96 0.00 39.81 5.34
3420 3597 4.488770 AGGTTGCCTCAAATCCCTAAAAA 58.511 39.130 0.00 0.00 0.00 1.94
3454 3631 9.599866 CAAGATTACACCTGACTAATTGACATA 57.400 33.333 0.00 0.00 0.00 2.29
3488 3684 6.648310 TGCGCATGAAGGAAAAATTTCATAAA 59.352 30.769 5.66 0.00 40.93 1.40
3491 3687 4.567971 TGCGCATGAAGGAAAAATTTCAT 58.432 34.783 5.66 0.00 42.98 2.57
3497 3693 2.562298 AGGAATGCGCATGAAGGAAAAA 59.438 40.909 26.09 0.00 0.00 1.94
3503 3699 6.310956 TGAAAAATTAAGGAATGCGCATGAAG 59.689 34.615 26.09 0.00 0.00 3.02
3510 3706 6.869421 ACGATTGAAAAATTAAGGAATGCG 57.131 33.333 0.00 0.00 0.00 4.73
3513 3709 9.124807 GAACGAACGATTGAAAAATTAAGGAAT 57.875 29.630 0.14 0.00 0.00 3.01
3516 3712 7.589954 ACTGAACGAACGATTGAAAAATTAAGG 59.410 33.333 0.14 0.00 0.00 2.69
3517 3713 8.409690 CACTGAACGAACGATTGAAAAATTAAG 58.590 33.333 0.14 0.00 0.00 1.85
3525 3721 3.057019 CTCCACTGAACGAACGATTGAA 58.943 45.455 0.14 0.00 0.00 2.69
3526 3722 2.609491 CCTCCACTGAACGAACGATTGA 60.609 50.000 0.14 0.00 0.00 2.57
3527 3723 1.726791 CCTCCACTGAACGAACGATTG 59.273 52.381 0.14 0.00 0.00 2.67
3528 3724 1.337823 CCCTCCACTGAACGAACGATT 60.338 52.381 0.14 0.00 0.00 3.34
3529 3725 0.246635 CCCTCCACTGAACGAACGAT 59.753 55.000 0.14 0.00 0.00 3.73
3531 3727 0.246635 ATCCCTCCACTGAACGAACG 59.753 55.000 0.00 0.00 0.00 3.95
3532 3728 2.474410 AATCCCTCCACTGAACGAAC 57.526 50.000 0.00 0.00 0.00 3.95
3533 3729 3.517901 ACATAATCCCTCCACTGAACGAA 59.482 43.478 0.00 0.00 0.00 3.85
3534 3730 3.104512 ACATAATCCCTCCACTGAACGA 58.895 45.455 0.00 0.00 0.00 3.85
3535 3731 3.543680 ACATAATCCCTCCACTGAACG 57.456 47.619 0.00 0.00 0.00 3.95
3536 3732 7.170998 CGTTAATACATAATCCCTCCACTGAAC 59.829 40.741 0.00 0.00 0.00 3.18
3537 3733 7.214381 CGTTAATACATAATCCCTCCACTGAA 58.786 38.462 0.00 0.00 0.00 3.02
3539 3735 5.932303 CCGTTAATACATAATCCCTCCACTG 59.068 44.000 0.00 0.00 0.00 3.66
3540 3736 5.605488 ACCGTTAATACATAATCCCTCCACT 59.395 40.000 0.00 0.00 0.00 4.00
3541 3737 5.861727 ACCGTTAATACATAATCCCTCCAC 58.138 41.667 0.00 0.00 0.00 4.02
3550 3763 4.500117 CGCAACTCGACCGTTAATACATAA 59.500 41.667 0.00 0.00 41.67 1.90
3566 3779 1.416813 CGGTCTCTCATGCGCAACTC 61.417 60.000 17.11 0.09 0.00 3.01
3577 3791 2.708386 ATATACTTGCGCGGTCTCTC 57.292 50.000 8.83 0.00 0.00 3.20
3586 3800 4.703897 TCCCTCCTCAAAATATACTTGCG 58.296 43.478 0.00 0.00 0.00 4.85
3628 3862 3.010420 AGAGGAAATTAGCGCCAAAGAC 58.990 45.455 2.29 0.00 0.00 3.01
3650 3884 4.841246 GGAGAAGGATTGCCTCTAGGATAA 59.159 45.833 0.00 0.00 46.28 1.75
3724 3970 4.256920 GCTCTAAGAACAGCAAGGAATCA 58.743 43.478 0.00 0.00 35.56 2.57
3777 4025 0.603707 TTTCTTCTGCGCCTGTGGAG 60.604 55.000 4.18 0.00 0.00 3.86
3784 4032 1.758783 CAACAACTTTCTTCTGCGCC 58.241 50.000 4.18 0.00 0.00 6.53
3790 4038 5.884771 AGAAGAACAGCAACAACTTTCTTC 58.115 37.500 12.41 12.41 46.67 2.87
3798 4046 1.593196 CCCGAGAAGAACAGCAACAA 58.407 50.000 0.00 0.00 0.00 2.83
3800 4048 0.884704 TGCCCGAGAAGAACAGCAAC 60.885 55.000 0.00 0.00 0.00 4.17
3806 4054 0.108567 GTCCTCTGCCCGAGAAGAAC 60.109 60.000 1.97 0.00 42.62 3.01
3814 4062 0.754957 AGATGAGAGTCCTCTGCCCG 60.755 60.000 0.60 0.00 40.61 6.13
3847 4098 0.933973 CGACAATTGTTTGCGCTGCA 60.934 50.000 13.36 1.48 36.22 4.41
3848 4099 1.768603 CGACAATTGTTTGCGCTGC 59.231 52.632 13.36 0.00 36.22 5.25
3849 4100 1.768603 GCGACAATTGTTTGCGCTG 59.231 52.632 26.65 0.00 45.86 5.18
3850 4101 4.226803 GCGACAATTGTTTGCGCT 57.773 50.000 26.65 0.00 45.86 5.92
3852 4103 1.007964 TGGGCGACAATTGTTTGCG 60.008 52.632 22.57 17.98 36.22 4.85
3853 4104 0.943835 GGTGGGCGACAATTGTTTGC 60.944 55.000 21.83 21.83 36.22 3.68
3854 4105 0.662970 CGGTGGGCGACAATTGTTTG 60.663 55.000 13.36 9.80 38.86 2.93
3855 4106 1.657556 CGGTGGGCGACAATTGTTT 59.342 52.632 13.36 0.00 0.00 2.83
3856 4107 2.265182 CCGGTGGGCGACAATTGTT 61.265 57.895 13.36 0.00 0.00 2.83
3857 4108 2.671619 CCGGTGGGCGACAATTGT 60.672 61.111 11.78 11.78 0.00 2.71
3858 4109 2.671619 ACCGGTGGGCGACAATTG 60.672 61.111 6.12 3.24 36.48 2.32
3859 4110 2.359478 GACCGGTGGGCGACAATT 60.359 61.111 14.63 0.00 36.48 2.32
3860 4111 3.319198 AGACCGGTGGGCGACAAT 61.319 61.111 14.63 0.00 34.63 2.71
3869 4120 4.838152 CGATGGGCCAGACCGGTG 62.838 72.222 14.63 0.00 40.62 4.94


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.